Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/7abef2f3637b0420f83c4d53b7760e/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/3fc0d6010e94edc8368394788cea8c/aih-tih-sc-387c73-R1_A23WJ53LT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/3fc0d6010e94edc8368394788cea8c/aih-tih-sc-387c73-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/3fc0d6010e94edc8368394788cea8c/aih-tih-sc-387c73-R1_A23WJ53LT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/7abef2f3637b0420f83c4d53b7760e/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/cd2251b0a828784d385959d760c1de/aih-tih-sc-387c73-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai ==> STAGING COMPLETE (7 inputs) 09:09:06 : INFO 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rate=13103225.81/min [6780000], rate=13122580.65/min [6790000], rate=13141935.48/min [6800000], rate=13161290.32/min [6810000], rate=13180645.16/min [6820000], rate=13200000.00/min [6830000], rate=13219354.84/min [6840000], rate=13238709.68/min [6850000], rate=13258064.52/min [6860000], rate=13277419.35/min [6870000], rate=13296774.19/min [6880000], rate=13316129.03/min [6890000], rate=13335483.87/min [6900000], rate=12937500.00/min [6910000], rate=12956250.00/min [6920000], rate=12975000.00/min [6930000], rate=12993750.00/min [6940000], rate=13012500.00/min [6950000], rate=13031250.00/min [6960000], rate=13050000.00/min [6970000], rate=13068750.00/min [6980000], rate=13087500.00/min [6990000], rate=13106250.00/min [7000000], rate=13125000.00/min [7010000], rate=13143750.00/min [7020000], rate=13162500.00/min [7030000], rate=13181250.00/min [7040000], rate=13200000.00/min [7050000], rate=13218750.00/min [7060000], rate=13237500.00/min [7070000], rate=13256250.00/min [7080000], rate=13275000.00/min [7090000], rate=13293750.00/min [7100000], rate=13312500.00/min [7110000], rate=13331250.00/min [7120000], rate=13350000.00/min [7130000], rate=12963636.36/min [7140000], rate=12981818.18/min [7150000], rate=13000000.00/min [7160000], rate=13018181.82/min [7170000], rate=13036363.64/min [7180000], rate=13054545.45/min [7190000], rate=13072727.27/min [7200000], rate=13090909.09/min [7210000], rate=13109090.91/min [7220000], rate=13127272.73/min [7230000], rate=13145454.55/min [7240000], rate=13163636.36/min [7250000], rate=13181818.18/min [7260000], rate=13200000.00/min [7270000], rate=13218181.82/min [7280000], rate=12847058.82/min [7290000], rate=12864705.88/min [7300000], rate=12882352.94/min [7310000], rate=12900000.00/min [7320000], rate=12917647.06/min [7330000], rate=12935294.12/min [7340000], rate=12952941.18/min [7350000], rate=12970588.24/min [7360000], rate=12617142.86/min [7370000], rate=12634285.71/min [7380000], rate=12651428.57/min [7390000], rate=12668571.43/min [7400000], rate=12685714.29/min [7410000], rate=12702857.14/min [7420000], rate=12720000.00/min [7430000], rate=12737142.86/min [7440000], rate=12754285.71/min [7450000], rate=12771428.57/min [7460000], rate=12788571.43/min [7470000], rate=12805714.29/min [7480000], rate=12822857.14/min [7490000], rate=12840000.00/min [7500000], rate=12857142.86/min [7510000], rate=12874285.71/min [7520000], rate=12891428.57/min [7530000], rate=12908571.43/min [7540000], rate=12925714.29/min [7550000], rate=12942857.14/min [7560000], rate=12960000.00/min [7570000], rate=12977142.86/min [7580000], rate=12994285.71/min [7590000], rate=12650000.00/min [7600000], rate=12666666.67/min [7610000], rate=12683333.33/min [7620000], rate=12700000.00/min [7630000], rate=12716666.67/min [7640000], rate=12733333.33/min [7650000], rate=12750000.00/min [7660000], rate=12766666.67/min [7670000], rate=12783333.33/min [7680000], rate=12800000.00/min [7690000], rate=12816666.67/min [7700000], rate=12833333.33/min [7710000], rate=12850000.00/min [7720000], rate=12866666.67/min [7730000], rate=12883333.33/min [7740000], rate=12900000.00/min [7750000], rate=12916666.67/min [7760000], rate=12933333.33/min [7770000], rate=12950000.00/min [7780000], rate=12966666.67/min [7790000], rate=12983333.33/min [7800000], rate=13000000.00/min [7810000], rate=13016666.67/min [7820000], rate=13033333.33/min [7830000], rate=13050000.00/min [7840000], rate=12713513.51/min [7850000], rate=12729729.73/min [7860000], rate=12745945.95/min [7870000], rate=12762162.16/min [7880000], rate=12778378.38/min [7890000], rate=12794594.59/min [7900000], rate=12810810.81/min [7910000], rate=12827027.03/min [7920000], rate=12843243.24/min [7930000], rate=12859459.46/min [7940000], rate=12875675.68/min [7950000], rate=12891891.89/min [7960000], rate=12908108.11/min [7970000], rate=12924324.32/min [7980000], rate=12940540.54/min [7990000], rate=12956756.76/min [8000000], rate=12972972.97/min [8010000], rate=12989189.19/min [8020000], rate=13005405.41/min [8030000], rate=13021621.62/min [8040000], rate=13037837.84/min [8050000], rate=13054054.05/min [8060000], rate=13070270.27/min [8070000], rate=13086486.49/min [8080000], rate=12757894.74/min [8090000], rate=12773684.21/min [8100000], rate=12789473.68/min [8110000], rate=12805263.16/min [8120000], rate=12821052.63/min [8130000], rate=12836842.11/min [8140000], rate=12852631.58/min [8150000], rate=12868421.05/min [8160000], rate=12884210.53/min [8170000], rate=12900000.00/min [8180000], rate=12915789.47/min [8190000], rate=12931578.95/min [8200000], rate=12947368.42/min [8210000], rate=12963157.89/min [8220000], rate=12978947.37/min [8230000], rate=12994736.84/min [8240000], rate=13010526.32/min [8250000], rate=13026315.79/min [8260000], rate=13042105.26/min [8270000], rate=13057894.74/min [8280000], rate=13073684.21/min 09:09:55 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-387c73-R1_A23WJ53LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-387c73-R1_A23WJ53LT4_1.cancer.introns.prelim Use of uninitialized value $ctat_genome_lib in concatenation (.) or string at /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl line 18. -aih-tih-sc-387c73-R1_A23WJ53LT4_1.introns: identified 6399 cancer introns 09:09:55 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-387c73-R1_A23WJ53LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-387c73-R1_A23WJ53LT4_1.cancer.introns.prelim 09:09:55 : INFO : Running: touch /tmp/nxf.m4MWe92IDr/aih-tih-sc-387c73-R1_A23WJ53LT4_1.chckpts/prelim_introns.ok 09:09:55 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-387c73-R1_A23WJ53LT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-387c73-R1_A23WJ53LT4_1.cancer.introns 09:09:56 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-387c73-R1_A23WJ53LT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-387c73-R1_A23WJ53LT4_1.cancer.introns 09:09:56 : INFO : Running: touch /tmp/nxf.m4MWe92IDr/aih-tih-sc-387c73-R1_A23WJ53LT4_1.chckpts/introns_filtered.ok 09:09:56 : INFO : -found 2717 cancer introns 09:09:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-387c73-R1_A23WJ53LT4_1.introns --cancer_introns aih-tih-sc-387c73-R1_A23WJ53LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-387c73-R1_A23WJ53LT4_1.introns.for_IGV.bed 09:09:56 : INFO : Creating the BED File. 09:10:04 : INFO : Saving Bed File as aih-tih-sc-387c73-R1_A23WJ53LT4_1.introns.for_IGV.bed 09:10:05 : INFO : Execution Time = 0.14 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-387c73-R1_A23WJ53LT4_1.introns --cancer_introns aih-tih-sc-387c73-R1_A23WJ53LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-387c73-R1_A23WJ53LT4_1.introns.for_IGV.bed 09:10:05 : INFO : Running: touch /tmp/nxf.m4MWe92IDr/aih-tih-sc-387c73-R1_A23WJ53LT4_1.chckpts/intron_igv_bed.ok 09:10:05 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-387c73-R1_A23WJ53LT4_1.introns.for_IGV.bed --bam aih-tih-sc-387c73-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-387c73-R1_A23WJ53LT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-387c73-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai 09:34:29 : INFO : Execution Time = 24.41 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-387c73-R1_A23WJ53LT4_1.introns.for_IGV.bed --bam aih-tih-sc-387c73-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-387c73-R1_A23WJ53LT4_1 09:34:29 : INFO : Running: touch /tmp/nxf.m4MWe92IDr/aih-tih-sc-387c73-R1_A23WJ53LT4_1.chckpts/reads_alignments_extracted.ok 09:34:29 : INFO : Running: samtools sort -o aih-tih-sc-387c73-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-387c73-R1_A23WJ53LT4_1.cancer_intron_reads.bam 09:34:30 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-387c73-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-387c73-R1_A23WJ53LT4_1.cancer_intron_reads.bam 09:34:30 : INFO : Running: touch /tmp/nxf.m4MWe92IDr/aih-tih-sc-387c73-R1_A23WJ53LT4_1.chckpts/sort_cancer_intron_reads.ok 09:34:30 : INFO : Running: samtools sort -o aih-tih-sc-387c73-R1_A23WJ53LT4_1.gene_reads.sorted.bam aih-tih-sc-387c73-R1_A23WJ53LT4_1.gene_reads.bam